When you define a partner you also define a connection for each of the partner flows, an inbound connection for the inbound flow and an outbound connection for the outbound flow.
In the inbound connection, you define the source from where B2B Gateway picks up files. In the outbound connection, you define the target where B2B Gateway places the files for the partner.
Configure connections in Administrator. For more information about configuring connections, see Connections in the Administrator help.